Literature DB >> 29354283

Regeneration in distantly related species: common strategies and pathways.

Maria Rita Fumagalli1,2, Stefano Zapperi1,3,4, Caterina A M La Porta2.   

Abstract

While almost all animals are able to at least partially replace some lost parts, regeneration abilities vary considerably across species. Here we study gene expression patterns in distantly related species to investigate conserved regeneration strategies. To this end, we collect from the literature transcriptomic data obtained during the regeneration of three species (Hydra magnipapillata, Schmidtea mediterranea, and Apostichopus japonicus), and compare them with gene expression during regeneration in vertebrates and mammals. This allows us to identify a common set of differentially expressed genes and relevant shared pathways that are conserved across species during the early stage of the regeneration process. We also find a set of differentially expressed genes that in mammals are associated to the presence of macrophages and to the epithelial-mesenchymal transition. This suggests that features of the sophisticated wound healing strategy of mammals are already observable in earlier emerging metazoans.

Entities:  

Year:  2018        PMID: 29354283      PMCID: PMC5764997          DOI: 10.1038/s41540-017-0042-z

Source DB:  PubMed          Journal:  NPJ Syst Biol Appl        ISSN: 2056-7189


  41 in total

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Open source clustering software.

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Journal:  Bioinformatics       Date:  2004-02-10       Impact factor: 6.937

Review 3.  Evolutionary loss of animal regeneration: pattern and process.

Authors:  Alexandra E Bely
Journal:  Integr Comp Biol       Date:  2010-08-19       Impact factor: 3.326

4.  Proteomics. Tissue-based map of the human proteome.

Authors:  Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén
Journal:  Science       Date:  2015-01-23       Impact factor: 47.728

5.  A molecular wound response program associated with regeneration initiation in planarians.

Authors:  Danielle Wenemoser; Sylvain W Lapan; Alex W Wilkinson; George W Bell; Peter W Reddien
Journal:  Genes Dev       Date:  2012-05-01       Impact factor: 11.361

Review 6.  Senescence-associated inflammatory responses: aging and cancer perspectives.

Authors:  Audrey Lasry; Yinon Ben-Neriah
Journal:  Trends Immunol       Date:  2015-03-21       Impact factor: 16.687

7.  A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.

Authors:  Donald M Bryant; Kimberly Johnson; Tia DiTommaso; Timothy Tickle; Matthew Brian Couger; Duygu Payzin-Dogru; Tae J Lee; Nicholas D Leigh; Tzu-Hsing Kuo; Francis G Davis; Joel Bateman; Sevara Bryant; Anna R Guzikowski; Stephanie L Tsai; Steven Coyne; William W Ye; Robert M Freeman; Leonid Peshkin; Clifford J Tabin; Aviv Regev; Brian J Haas; Jessica L Whited
Journal:  Cell Rep       Date:  2017-01-17       Impact factor: 9.423

Review 8.  Preparing the ground for tissue regeneration: from mechanism to therapy.

Authors:  Stuart J Forbes; Nadia Rosenthal
Journal:  Nat Med       Date:  2014-08       Impact factor: 53.440

9.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

10.  CD-HIT: accelerated for clustering the next-generation sequencing data.

Authors:  Limin Fu; Beifang Niu; Zhengwei Zhu; Sitao Wu; Weizhong Li
Journal:  Bioinformatics       Date:  2012-10-11       Impact factor: 6.937

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  11 in total

Review 1.  Animal regeneration in the era of transcriptomics.

Authors:  Loïc Bideau; Pierre Kerner; Jerome Hui; Michel Vervoort; Eve Gazave
Journal:  Cell Mol Life Sci       Date:  2021-01-30       Impact factor: 9.261

2.  The Rapid Regenerative Response of a Model Sea Anemone Species Exaiptasia pallida Is Characterised by Tissue Plasticity and Highly Coordinated Cell Communication.

Authors:  Chloé A van der Burg; Ana Pavasovic; Edward K Gilding; Elise S Pelzer; Joachim M Surm; Hayden L Smith; Terence P Walsh; Peter J Prentis
Journal:  Mar Biotechnol (NY)       Date:  2020-02-03       Impact factor: 3.619

Review 3.  The Hazards of Regeneration: From Morgan's Legacy to Evo-Devo.

Authors:  Chiara Sinigaglia; Alexandre Alié; Stefano Tiozzo
Journal:  Methods Mol Biol       Date:  2022

4.  JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration.

Authors:  Ping-Lin Cao; Nobuyoshi Kumagai; Takeshi Inoue; Kiyokazu Agata; Takashi Makino
Journal:  Genome Biol Evol       Date:  2019-02-01       Impact factor: 3.416

5.  Understanding the Metabolic Profile of Macrophages During the Regenerative Process in Zebrafish.

Authors:  Lais Cavalieri Paredes; Niels Olsen Saraiva Camara; Tarcio Teodoro Braga
Journal:  Front Physiol       Date:  2019-05-24       Impact factor: 4.566

Review 6.  Regenerative medicine meets mathematical modelling: developing symbiotic relationships.

Authors:  S L Waters; L J Schumacher; A J El Haj
Journal:  NPJ Regen Med       Date:  2021-04-12

Review 7.  Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi.

Authors:  Allison Edgar; Dorothy G Mitchell; Mark Q Martindale
Journal:  Genes (Basel)       Date:  2021-06-05       Impact factor: 4.096

Review 8.  Beyond Adult Stem Cells: Dedifferentiation as a Unifying Mechanism Underlying Regeneration in Invertebrate Deuterostomes.

Authors:  Cinzia Ferrario; Michela Sugni; Ildiko M L Somorjai; Loriano Ballarin
Journal:  Front Cell Dev Biol       Date:  2020-10-20

Review 9.  The Role of Macrophages During Zebrafish Injury and Tissue Regeneration Under Infectious and Non-Infectious Conditions.

Authors:  Candice Bohaud; Matt D Johansen; Christian Jorgensen; Natacha Ipseiz; Laurent Kremer; Farida Djouad
Journal:  Front Immunol       Date:  2021-07-21       Impact factor: 7.561

Review 10.  The Tentacular Spectacular: Evolution of Regeneration in Sea Anemones.

Authors:  Chloé A van der Burg; Peter J Prentis
Journal:  Genes (Basel)       Date:  2021-07-14       Impact factor: 4.096

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